Flux balance analysis is a mathematical approach for analyzing the flow of metabolites through a metabolic network.
Recommanded review papers:
- Park, J. M., Kim, T. Y., & Lee, S. Y. (2009). Constraints-based genome-scale metabolic simulation for systems metabolic engineering. Biotechnology advances, 27(6), 979-988.
- Orth JD, Thiele I, Palsson BĂ. What is flux balance analysis?. Nature biotechnology. 2010 Mar;28(3):245-8.
Applications in systems metabolic engineering
Predict gene knockouts that allow an organism to produce desirable compounds.
- Burgard, A. P., Pharkya, P., & Maranas, C. D. (2003). Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnology and bioengineering, 84(6), 647-657. [paper]
- Feist AM, Zielinski DC, Orth JD, et al. Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli. Metabolic Engineering. 2010 May;12(3):173-186. DOI: 10.1016/j.ymben.2009.10.003. [paper]
Softwares/Tools for (non)linear optimization
| Tool | Language | Feature | Additional Info |
|---|---|---|---|
| CasADi | Octav; Matlab; Python; C++ | Algorithmic differentiation; Export conputating graph to stand-alone C code | Â |
| Ipopt | C++ | Sparsed calculation | Interior Point OPTimizer (IPOPT) |
| cyipopt | Python | Sparsed calculation | A Python wrapper around Ipopy |
- Mixed-integer linear programming (MILP).